Introduction | Installation | Example workflow | 1. Load example ChIP-seq peak sets (genomic) | 2. Compute overlaps between genomic regions | 3. Visualization | Venn diagram | UpSet plot | Export visualization | 4. Extract elements per overlap group | Overlap group naming | Extract one particular group | Export overlap groups | For all overlap types (genomic or gene sets): | For genomic overlaps only: | Customization examples | Custom fills with transparency | Colored edges, no fills (colored borders only) | Custom labels and counts + percentages | Legend at the bottom with custom text | Combining multiple custom options | Session info | References | Example A549 ChIP-seq dataset | Supporting packages
Package: gVenn 1.3.2
Christophe Tav
gVenn: Proportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions
Tools to compute and visualize overlaps between gene sets or genomic regions. Venn diagrams with proportional areas are provided, while UpSet plots are recommended for larger numbers of sets. The package supports GRanges and GRangesList inputs, and integrates with analysis workflows for ChIP-seq, ATAC-seq, and other genomic interval data. It generates clean, interpretable, and publication-ready figures.
Authors:
gVenn_1.3.2.tar.gz
gVenn_1.3.2.zip(r-4.7)gVenn_1.3.2.zip(r-4.6)gVenn_1.3.2.zip(r-4.5)
gVenn_1.3.2.tgz(r-4.6-any)gVenn_1.3.2.tgz(r-4.5-any)
gVenn_1.3.2.tar.gz(r-4.7-any)gVenn_1.3.2.tar.gz(r-4.6-any)
gVenn_1.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gVenn/json (API)
| # Install 'gVenn' in R: |
| install.packages('gVenn', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ckntav/gvenn/issues
Pkgdown/docs site:https://ckntav.github.io
Datasets:
- a549_chipseq_peaks - A549 ChIP-seq Consensus Peak Subsets
- gene_list - Example Gene Lists with Overlaps
On BioConductor:gVenn-1.3.2(bioc 3.24)gVenn-1.1.1(bioc 3.23)
softwarevisualizationchipseqatacseqepigeneticsdatarepresentationsequencing
Last updated from:8ea4fed992. Checks:1 WARNING, 2 ERROR, 7 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 210 | ||
| linux-devel-x86_64 | ERROR | 228 | ||
| source / vignettes | OK | 273 | ||
| linux-release-x86_64 | OK | 299 | ||
| macos-release-arm64 | OK | 111 | ||
| macos-oldrel-arm64 | OK | 113 | ||
| windows-devel | ERROR | 171 | ||
| windows-release | OK | 129 | ||
| windows-oldrel | OK | 131 | ||
| wasm-release | OK | 186 |
Exports:computeOverlapsexportOverlapsexportOverlapsToBedextractOverlapsplotUpSetplotVennsaveViztoday
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDelayedArraydigestdoParalleleulerrforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesGetoptLongGlobalOptionsgluehttrIRangesiteratorsjsonlitelambda.rlatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsystimechangevctrswritexlXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A549 ChIP-seq Consensus Peak Subsets (Dex, chr7) | a549_chipseq_peaks |
| Compute Overlaps Between Multiple Sets or Genomic Regions | computeOverlaps |
| Export Overlap Groups to Excel | exportOverlaps |
| Export Overlap Groups to BED Files | exportOverlapsToBed |
| Extract Overlap Groups from Genomic or Set Overlap Results | extractOverlaps |
| Example Gene Lists with Overlaps | gene_list |
| Plot an UpSet Diagram from Genomic or Set Overlap Results | plotUpSet |
| Plot a Venn Diagram from Genomic or Set Overlap Results | plotVenn |
| Save a Visualization to File (PDF, PNG, or SVG) | saveViz |
| Today's Date at Package Load Time | today |
